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Genes and Evolution
Molecular clocks and phylogenies
Adam Price
Systematics A definition of taxonomyPhylogenies Characters and traits
Homology and homoplastySimple PhylogeniesMolecular evolution
SubstitutionsSynonymous and nonsynonymous Selection and neutral theory
Molecular phylogeniesMolecular clocks
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Defining Systematics and Taxonomy
Systematics- the study of the diversity of organisms
Taxonomy- the science of classification of organismstaxis = Greek to arrange, classify
Why?Explains evolutionary relationshipsIntrinsically interestedUnderpins an understanding of biology- e.g. ecology, conservationImportant in applications to human life
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Phylogeny- the history of descent of a group of organisms from a common ancestor
from Greek- phylon = tribe, race genesis = source
Conventionally represented by a phylogeneic treeMonkey
Gorilla
Chimpanzee
Human
Ferns
Conifers
Peas
Rice
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Phylogenic trees
Phylogentic trees are based on comparison of traitsindividuals with common traits are placed together
Traits inherited from a common ancestor are termed homologous
Traits that differs from the ancestor are termed derived
Phylogenies are trees that best explain the distribution of homologous and derived traits in the organisms studied (the focal group).
Character = a feature of the organisms (e.g. flower colour, height)Trait = one form of a character (blue flower colour, short height)
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Derived trait
TaxonJaws Lungs Claws or
nailsFeathers Fur Mammary
glandsFour-chambered
heartHagfish - - - - - - -Perch + - - - - - -Salamander + + - - - - -Lizard + + + - - - -Crocodile + + + - - - +Pigeon + + + + - - +Mouse + + + - + + +Chimpanzee + + + - + + +
Scoring traits to make a simple phylogeny
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Hagfish
Perch
Salamander
Lizard
Crocodile
Pigeon
Mouse
Chimpanzee
Jaws
Lungs
Claws ornails
Four-chamberedheart
Fur, mammaryglands
Feathers
A simple phylogeny
Relative evolutionary time
Ancient events Recent events
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Monophyletic
Paraphyletic
Polyphyletic
Monophyletic taxa include all descendants of a common ancestorParaphyletic taxa include some, but not all, descendants of a common ancestorPolyphyletic taxa includes members with more than one recent common ancestor
Outgroup
Outgroup a lineage closely related to the focal group
Phylogenetic trees
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The problem of homoplastic traitstraits that appear similar but are not related through ancestry
Convergent evolution- independent evolution of similar traits due to similar selection pressure (e.g. wings in birds and bats)
Parallel evolution- independent evolution of common traits in organisms sharing distant relatives (e.g. patterns of butterfly wings).
Evolutionary reversals- the loss of a derived trait (e.g. limbs of snakes, teeth of frogs).
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Traits used in phylogenetics
Morphology and developmentalthe importance of fossils
MolecularProtein sequencesGenetic markersDNA sequences
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The advantages of molecular traits
Disadvantages ?
1/ They directly reflect the underlying process of evolution- changes in the hereditary material
2/ There are a vast number of potential traits
3/ They can detect difference between very closely related organism (even those that show no phenotypic difference)
4/ They are not effected by the environment (unlike some morphological traits)
5/ Since mutations generally occur as random events with specific probabilities, the number of mutations can be used to calibrate evolutionary time (molecular clocks)
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Transitions and Transversions in nucleotide substitutions
Transitions replace a purine base with the other purine base, or a pyrimidine base with the other pyrimidine base
Pyrimidines T C C TPurines A G G A
Transversions replace a purine with a pyrimidine or vice versa
T A T G C A C GA T A C G T G C
Transition mutations are about 2 x more common than transversions
A
TC
G Transition
Transition
Transversion
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Mutation in Coding vs Noncoding DNA
Mutations in noncoding DNA do not generally effect phenotype and therefore are not subjected to selection
A substantial part of the DNA of eukaryotes is noncoding- introns, repetitive sequences, pseudogenes
Some mutations in coding regions do not change amino acid sequence because of the degenerate codon system
Some mutations in coding regions change amino acid sequence to a similar type of amino acid, therefore having little or no effect on protein function
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Synonymous vs nonsynonymous substitutions
Substitutions in Coding regions
Synonymous substitutions are those that do not change the amino acid that is specified by the gene
There are various degrees of nonsynonymous mutations depending on there effect on protein function. When the mutation changes the amino acid to a similar type then function may be little effected. Some amino acids of proteins are more important than others- active sites for example.
CUU ----> AUU = Leucine -----> Isoleucine
Nonsynonymous substitutions are those that change the amino acid chain specified
CUU ----> CUC = Leucine -----> Leucine
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Miss-sense substitutions
Substitutions in Coding regions
Miss-sense substitutions are those that prematurely terminate the gene
UAU ----> UAG = Tyrosine -----> Stop
UUA ----> UAA = Leucine -----> Stop
Generally rare since nearly always involved change in protein activity
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U C A GUUU UCU UAU UGUUUC
Phenyl-alanineF UCC UAC
TyrosineYUGC
CystineC
UUA UCA UAA UGA Stop
U
UUGLeucineL
UCG
SerineS
UAGStop
UGG TryptophanWCUU CCU CAU CGUCUC CCC CAC
HistidineHCGC
CUA CCA CAA CGA
C
CUG
LeucineL
CCG
ProlineP
CAGGlutamineQ
CGG
ArginineR
AUU ACU AAU AGUAUC ACC AAC
AsparagineNAGC
SerineS
AUAIsoleucineI
ACA AAA AGA
A
AUG MethionineM ACG
ThreonineT
AAGLysineK
AGGArginineR
GUU GCU GAU GGUGUC GCC GAC
AspaticacidD GGC
GUA GCA GAA GGA
G
GUG
ValineV
GCG
AlanineA
GAGGlutamicacidE GGG
GlycineG
Second Letter
Fir
st L
ette
r
Codon usage
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0
2
4
6
8
10
12S
ub
stit
uti
on
s p
er
site
pe
r 10
00,0
00,0
00 y
ea
rsSynonymous mutationsNonsynonymous mutations
Synonymous mutations are more commonly fixed in evolution
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0
1
2
3
4
5
6
7
8
9
10
Su
bst
itu
tio
ns
pe
r si
te p
er
1000
,000
,000
ye
ars
Ups
trea
m r
egio
ns
Dow
nstr
eam
reg
ions
Non
-deg
ener
ate
site
s
Tw
ofol
d de
gene
rate
sit
es
Fou
rfol
d de
gene
rate
sit
es
Intr
ons
Pse
udog
enes
Ani
mal
mtD
NA
Different types of sequence evolve at different rates
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Comparing amino acid sequences
leu arg phe cys ser arg
leu gap phe cys phe arg
leu gap phe cys phe arg
leu arg ile cys ser argleu arg ile cys ser arg
leu arg phe cys ser arg
ser
ser
ser
serala
ile
Sequence 1Sequence 2Sequence 3Sequence 4Sequence 5Sequence 6
leu arg phe cys ser arg
leu gap phe cys ser arg
ser
ser
Sequence 1Sequence 2
leu arg phe cys ser arg
leu phe cys ser arg
ser
ser
Sequence 1Sequence 2
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leu arg phe cys ser arg
leu gap phe cys phe arg
leu gap phe cys phe arg
leu arg ile cys ser argleu arg ile cys ser arg
leu arg phe cys ser arg
ser
ser
ser
serala
ile
Sequence 1Sequence 2Sequence 3Sequence 4Sequence 5Sequence 6
1 2 3 4 5 6
1 2 2 1 2 1
2 5 0 3 4 3
3 5 7 3 4 3
4 6 4 4 1 2
5 5 3 3 6 2
6 6 4 4 5 5
Sequence NumberDifferences
Similarities
Comparing amino acid sequences
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Human/chimp G D V E K G K K I F I M K C S Q C H T V E K G G K H K T G P N L H G L F G R K T G Q A P G Y S YRhesus monkey G D V E K G K K I F I M K C S Q C H T V E K G G K H K T G P N L H G L F G R K T G Q A P G Y S Y
Horse G D V E K G K K I F V Q K C A Q C H T V E K G G K H K T G P N L H G L F G R K T G Q A P G F T YDonkey G D V E K G K K I F V Q K C A Q C H T V E K G G K H K T G P N L H G L F G R K T G Q A P G F S Y
Cow G D V E K G K K I F V Q K C A Q C H T V E K G G K H K T G P N L H G L F G R K T G Q A P G F S YDog G D V E K G K K I F V Q K C A Q C H T V E K G G K H K T G P N L H G L F G R K T G Q A P G F S Y
Rabbit G D V E K G K K I F V Q K C A Q C H T V E K G G K H K T G P N L H G L F G R K T G Q A V G F S YGray whale G D V E K G K K I F V Q K C A Q C H T V E K G G K H K T G P N L H G L F G R K T G Q A V G F S Y
Grey kangaroo G D V E K G K K I F V Q K C A Q C H T V E K G G K H K T G P N L N G L F G R K T G Q A P G F T Y
Chicken G D I E K G K K I F V Q K C S Q C H T V E K G G K H K T G P N L H G L F G R K T G Q A E G F S YPigeon G D I E K G K K I F V Q K C S Q C H T V E K G G K H K T G P N L H G L F G R K T G Q A E G F S YDuck G D V E K G K K I F V Q K C S Q C H T V E K G G K H K T G P N L H G L F G R K T G Q A E G F S YTurtle G D V E K G K K I F V Q K C A Q C H T V E K G G K H K T G P N L N G L I G R K T G Q A E G F S YSnake G D V E K G K K I F T M K C S Q C H T V E K G G K H K T G P N L H G L F G R K T G Q A V G Y S YFrog G D V E K G K K I F V Q K C A Q C H T C E K G G K H K V G P N L Y G L I G R K T G Q A A G F S YTuna G D V A K G K K T F V Q K C A Q C H T V E N G G K H K V G P N L W G L F G R K T G Q A E G Y S Y
Dogfish G D V E K G K K V F V Q K C A Q C H T V E N G G K H K T G P N L S G L F G R K T G Q A Q G F S Y
Samia moth G N A E N G K K I F V Q R C A Q C H T V E A G G K H K V G P N L H G F Y G R K T G Q A P G F S YHornworm moth G N A D N G K K I F V Q R C A Q C H T V E A G G K H K V G P N L H G F F G R K T G Q A P G F S YScrew worm fly G D V E K G K K I F V Q R C A Q C H T V E A G G K H K V G P N L H G L F G R K T G Q A A G F A Y
Fruit fly G D V E K G K K L F V Q R C A Q C H T V E A G G K H K V G P N L H G L I G R K T G Q A A G F A YBakers yeast G S A K K G A T L F K T R C E L C H T V E K G G P H K V G P N L H G I F G R H S G Q A P G Y S Y
Candida krusei (yeast) G S A K K G A T L F K T R C A E C H T V E A G G P H K V G P N L H G I F G R H S G Q A P G Y S YNeursopora (mold) G D S K K G A N L F K T R C A E C H E N L T Q K I G P A L H G L F G R K T G Q A D G Y A Y
Wheat G N P D A G A K I F K T K C A Q C H T V E A G A H K Q G P N L H G L F G R Q S G S T A G Y S YSunflower G D P T T G A K I F K T K C A Q C H T V E K G A H K Q G P N L N G L F G R Q S G T T A G Y S Y
Mung bean G D S K S G E K I F K T K C A Q C H T V E K G A H K Q G P N L N G L F G R Q S G T T A G Y S YRice G N P K A G E K I F K T K C A Q C H T V E K G A H K Q G P N L N G L F G R Q S G T T P G Y S Y
Sesame G D V K S G E K I F K T K C A Q C H T V E K G A H K Q G P N L N G L F G R Q S G T T P G Y S Y
Cytochrome C- a highly conserved gene
Acidic side chains Basic side chainsHydrophobic side
chains
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0
10
20
30
40
50
60
0 200 400 600 800 1000 1200
Time since divergence (millions of years)
Am
ino
acid
sub
stit
utio
ns (
per
100
resi
dues
) in
cyt
ochr
ome
c
Yeast vs mould
Angiosperms vs animals
Insects vs vertebrates
Fish vs land vertebrates
Amphibians vs birds and mammals
Birds vs mammals
Mammals vs reptiles
Birds vs reptiles
A molecular clock for Cytochrome c
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The Neutral Theory of molecular evolution
Most mutations are either selectively neutral or nearly so.
Thus, the genetic variation within species results from random genetic drift
Consider population of size N with a neutral mutation rate at a locus of mutations per gamete per generation
No. of new mutations = x 2N
Probability of fixation by genetic drift = frequency, p = 1/2N
Number of new mutations per generation that are likely to become fixed by genetic drift = no. of mutations x probability of fixation
=
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The rate of fixation of neutral mutations is equal to the neutral mutation rate
Molecular clocks
Thus, sequences diverge in evolution at a constant rate
Thus, the divergence between two sequences can be used to say when the two organisms diverged from each other
But remember•Not all mutations are neutral•Not all loci change at the same rate•Transitions are more common than transversions•Rates are strictly based on generations (not years), and reproductive rates vary between species
Therefore, all molecular clocks need calibrating
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600
500
400
300
200
100
0
Mil
lion
yea
rsag
o
Species
Divergence based on molecular clockDivergence based on fossil record
Divergence of humans from other species based on -globin molecular clock calibrated on fossil evidence of divergence from cows
Calibration of -globin molecular clock
Shark
Carp
Frog
AlligatorChicken
QuollCow
Baboon